DIALIGN •
While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. [less]

GENIO/logo •
Positional dependent information contents of aligned RNA/DNA or amino acid sequences are useful for the display of consensus sequences and for finding optimal search windows used in sequence analysis. The program calculates the positional information content of mono or poly nucleotides/amino acids from a FASTA file of aligned sequences and writes a Postscript (or encapsulated Postscript, EPS) file that can be viewed and included in text processors [less]

MADAP •
MADAP is a flexible clustering tool for the interpretation of one-dimensional genome annotation data. Such data might consist of counts, probabilities, or intensities associated with genome positions. They may be generated by mapping mRNA 5' and 3' sequence tags to genomes, by ChIP-chip or ChIP-Seq assays, or by genome-wide genotype-phenotype association studies. MADAP identifies clusters of data points corresponding to genomic features. [less]

MaxAlign •
The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies.
MaxAlign maximizes the number of characters that are present in gap-free columns. It can be used prior to any phylogenetic analysis as well as in other situations where this form of alignment clean up is useful, such as the presence of badly aligned or truncated sequences.
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Newick Utilities •
The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. [less]

Phylogibbs •
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy. [less]

SIBsim4 •
SIBsim4 is a modified version of the sim4 program, which is a similarity-based tool for spliced alignments, i.e. for aligning an expressed DNA sequence (EST, mRNA) with a genomic sequence. [less]

WebLogo •
Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. [less]